Surely this is a fundamental flaw of the basic design? Everything is standard: The direction of the glass, the level of the cameras, the position of the light.
This might be better discussed with the designers of the book scanner in question, or a book scanner user group. CHDK is general purpose software for the camera, we aren't connected with whoever designed the book scanner.
A few random, of the top of my head ideas
Make the light source more diffuse.
If the reflection light doesn't saturate, you might be able to take picture with just the reflection on a black background and subtract it out in your image processing pipeline.
You can get ant-glare filters, for computer monitors for example. No idea if they would work in this situation.
